9OER | pdb_00009oer

HalA with lysine, Fe(II), chloride, and a peroxyhemiketal intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.201 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Dynamic metal coordination controls chemoselectivity in a radical halogenase.

Kissman, E.N.Kipouros, I.Slater, J.W.Stone, E.A.Yang, A.Y.Braun, A.Ensberg, A.R.Whitten, A.M.Chatterjee, K.Bogacz, I.Yano, J.Martin Bollinger Jr., J.Chang, M.C.Y.

(2026) Nat Chem Biol 22: 491-500

  • DOI: https://doi.org/10.1038/s41589-025-02077-x
  • Primary Citation Related Structures: 
    9OER, 9OES, 9OET, 9OEU, 9OEV, 9OEW

  • PubMed Abstract: 

    The activation of inert C(sp 3 )-H bonds by nonheme Fe enzymes provides a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp 3 complexity. In this context, Fe II /α-ketoglutarate-dependent radical halogenases are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide experimental evidence that bifurcation of radical rebound after H-atom abstraction can be driven both by the ability of a dynamic metal coordination sphere to reorganize and by a second-sphere hydrogen-bonding network where only two residues are sufficient. In addition, we present crystallographic data supporting the existence of an early peroxyhemiketal intermediate in the O 2 activation pathway of Fe II /α-ketoglutarate-dependent enzymes. These data provide a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields insight into the design principles by which to expand their reaction scope.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Berkeley, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 241.59 kDa 
  • Atom Count: 16,420 
  • Modeled Residue Count: 2,014 
  • Deposited Residue Count: 2,064 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine halogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
258Actinoplanes teichomyceticusMutation(s): 0 
Gene Names: FHX34_1011265
UniProt
Find proteins for A0A561WR11 (Actinoplanes teichomyceticus)
Explore A0A561WR11 
Go to UniProtKB:  A0A561WR11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A561WR11
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YL0
(Subject of Investigation/LOI)

Query on YL0



Download:Ideal Coordinates CCD File
GA [auth G],
Q [auth C],
U [auth D]
(4R)-4-chloro-L-lysine
C6 H13 Cl N2 O2
RARMVOFXKPZWMG-UHNVWZDZSA-N
A1CA1
(Subject of Investigation/LOI)

Query on A1CA1



Download:Ideal Coordinates CCD File
Z [auth E](2S)-2-hydroperoxy-2-hydroxypentanedioic acid
C5 H8 O7
IHRVEKFTFSYRQQ-YFKPBYRVSA-N
LYS
(Subject of Investigation/LOI)

Query on LYS



Download:Ideal Coordinates CCD File
CA [auth F],
I [auth A],
KA [auth H],
M [auth B],
Y [auth E]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
AKG
(Subject of Investigation/LOI)

Query on AKG



Download:Ideal Coordinates CCD File
J [auth A],
V [auth D]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SIN
(Subject of Investigation/LOI)

Query on SIN



Download:Ideal Coordinates CCD File
DA [auth F],
HA [auth G],
LA [auth H],
N [auth B],
R [auth C]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
AA [auth E]
EA [auth F]
IA [auth G]
K [auth A]
MA [auth H]
AA [auth E],
EA [auth F],
IA [auth G],
K [auth A],
MA [auth H],
O [auth B],
S [auth C],
W [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
BA [auth E]
FA [auth F]
JA [auth G]
L [auth A]
NA [auth H]
BA [auth E],
FA [auth F],
JA [auth G],
L [auth A],
NA [auth H],
P [auth B],
T [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.3α = 90
b = 147.3β = 90
c = 287.87γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDOE/LBL DEAC02-05CH11231 FWP CH030201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134271

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references
  • Version 1.2: 2026-03-18
    Changes: Database references